Variant report

Variant	rs188401427
Chromosome Location	chr5:52776175-52776176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr5:52776133-52776373	HepG2	liver:	n/a	chr5:52776291-52776302
2	CHD1	chr5:52773963-52779659	IMR90	lung:	n/a	chr5:52776596-52776606 chr5:52777700-52777710 chr5:52776601-52776611
3	POLR2A	chr5:52775052-52780368	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr5:52774386-52777094	HepG2	liver:	n/a	n/a
5	MAZ	chr5:52775488-52776469	HepG2	liver:	n/a	chr5:52776181-52776191 chr5:52775968-52775978 chr5:52775515-52775525
6	POLR2A	chr5:52776149-52776831	HepG2	liver:	n/a	n/a
7	GATA3	chr5:52774106-52777467	SK-N-SH	brain:	n/a	chr5:52774928-52774936 chr5:52776733-52776741
8	MAX	chr5:52775297-52776857	A549	lung:	n/a	chr5:52776181-52776191 chr5:52775968-52775978 chr5:52775515-52775525
9	HA-E2F1	chr5:52775601-52776748	Hela-S3	cervix:	n/a	chr5:52775806-52775821
10	TAF1	chr5:52776174-52776464	H1-hESC	embryonic stem cell:	n/a	n/a
11	MXI1	chr5:52775095-52779435	IMR90	lung:	n/a	n/a
12	POLR2A	chr5:52775948-52776938	Gliobla	brain:	n/a	n/a
13	CEBPD	chr5:52775893-52776567	HepG2	liver:	n/a	n/a
14	ZBTB7A	chr5:52776170-52776961	ECC-1	luminal epithelium:	n/a	n/a
15	TAF1	chr5:52775361-52776534	SK-N-SH	brain:	n/a	n/a
16	MAX	chr5:52775390-52776567	SK-N-SH	brain:	n/a	chr5:52776181-52776191 chr5:52775968-52775978 chr5:52775515-52775525
17	HEY1	chr5:52774155-52777346	HepG2	liver:	n/a	chr5:52776435-52776450 chr5:52776602-52776617 chr5:52774757-52774772
18	POLR2A	chr5:52774375-52780496	HepG2	liver:	n/a	n/a
19	NFIC	chr5:52775149-52776398	SK-N-SH	brain:	n/a	n/a
20	ZBTB7A	chr5:52775915-52776550	HepG2	liver:	n/a	chr5:52775986-52775995
21	CREB1	chr5:52775303-52776721	HepG2	liver:	n/a	n/a
22	POLR2A	chr5:52776162-52776922	HepG2	liver:	n/a	n/a
23	MYBL2	chr5:52775968-52776546	HepG2	liver:	n/a	n/a
24	FOXA1	chr5:52775803-52776468	HepG2	liver:	n/a	n/a
25	MXI1	chr5:52775617-52776848	HepG2	liver:	n/a	n/a
26	MAX	chr5:52775298-52776853	HepG2	liver:	n/a	chr5:52776181-52776191 chr5:52775968-52775978 chr5:52775515-52775525
27	FOXA2	chr5:52775954-52776333	HepG2	liver:	n/a	n/a
28	CHD2	chr5:52776171-52776498	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr5:52776161-52776981	Hela-S3	cervix:	n/a	n/a
30	PBX3	chr5:52775296-52776526	SK-N-SH	brain:	n/a	n/a
31	EP300	chr5:52775176-52777032	SK-N-SH	brain:	n/a	chr5:52775256-52775265 chr5:52775427-52775441 chr5:52775543-52775552 chr5:52776515-52776531 chr5:52775383-52775397
32	ZBTB7A	chr5:52775389-52776862	ECC-1	luminal epithelium:	n/a	chr5:52775986-52775995
33	SIN3AK20	chr5:52775900-52776499	SK-N-SH	brain:	n/a	n/a
34	HEY1	chr5:52775021-52777484	HepG2	liver:	n/a	chr5:52776435-52776450 chr5:52776602-52776617
35	POLR2A	chr5:52774388-52779438	IMR90	lung:	n/a	n/a
36	HDAC2	chr5:52775869-52776618	HepG2	liver:	n/a	chr5:52776307-52776326
37	POLR2A	chr5:52775353-52776896	HepG2	liver:	n/a	n/a
38	MAX	chr5:52775312-52776542	SK-N-SH	brain:	n/a	chr5:52776181-52776191 chr5:52775968-52775978 chr5:52775515-52775525
39	PBX3	chr5:52775232-52776606	SK-N-SH	brain:	n/a	n/a
40	E2F6	chr5:52776156-52776569	A549	lung:	n/a	n/a
41	REST	chr5:52775054-52776520	HepG2	liver:	n/a	n/a
42	TCF12	chr5:52775087-52776554	A549	lung:	n/a	chr5:52775338-52775346
43	CREB1	chr5:52775964-52776677	H1-hESC	embryonic stem cell:	n/a	n/a
44	CHD2	chr5:52775573-52776816	HepG2	liver:	n/a	chr5:52776596-52776606 chr5:52776601-52776611
45	POLR2A	chr5:52775032-52776803	HepG2	liver:	n/a	n/a
46	GATA3	chr5:52775278-52776540	SK-N-SH	brain:	n/a	n/a
47	TAF1	chr5:52775916-52776209	HepG2	liver:	n/a	n/a
48	FOXA1	chr5:52776009-52776447	HepG2	liver:	n/a	n/a
49	POLR2A	chr5:52776153-52776830	SK-N-SH	brain:	n/a	n/a
50	MAX	chr5:52775461-52776465	Hela-S3	cervix:	n/a	chr5:52776181-52776191 chr5:52775968-52775978 chr5:52775515-52775525

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:56735383..56737636-chr5:52775178..52776995,2	MCF-7	breast:

Variant related genes	Relation type
FST	TF binding region
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv328038	chr5:52772280-52777292	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
5	esv3412161	chr5:52775245-52777493	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52774200-52776600	Active TSS	H1 Cell Line	embryonic stem cell
2	chr5:52774200-52776600	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr5:52774200-52776600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr5:52774200-52776600	Active TSS	Ovary	ovary
5	chr5:52774200-52776600	Active TSS	Stomach Smooth Muscle	stomach
6	chr5:52774200-52776800	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr5:52774200-52776800	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr5:52774200-52776800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr5:52774200-52777200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr5:52774200-52777400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:52774200-52778200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:52774200-52778800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:52774200-52778800	Active TSS	Osteobl	bone
14	chr5:52774200-52779000	Active TSS	Colon Smooth Muscle	Colon
15	chr5:52774200-52779200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr5:52774400-52776600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr5:52774400-52776600	Active TSS	Muscle Satellite Cultured Cells	--
18	chr5:52774400-52776600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:52774400-52776600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:52774400-52776600	Active TSS	Esophagus	oesophagus
21	chr5:52774400-52776600	Active TSS	Pancreas	Pancrea
22	chr5:52774400-52776600	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr5:52774400-52776600	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr5:52774400-52776600	Active TSS	NH-A	brain
25	chr5:52774400-52778200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:52774400-52778400	Active TSS	Right Ventricle	heart
27	chr5:52774400-52778400	Bivalent/Poised TSS	Thymus	Thymus
28	chr5:52774400-52778600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:52774400-52778600	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr5:52774400-52778600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:52774400-52778600	Active TSS	Aorta	Aorta
32	chr5:52774400-52778800	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr5:52774400-52778800	Active TSS	Hela-S3	cervix
34	chr5:52774400-52778800	Active TSS	HSMM	muscle
35	chr5:52774400-52778800	Active TSS	HSMMtube	muscle
36	chr5:52774400-52778800	Active TSS	NHDF-Ad	bronchial
37	chr5:52774400-52779000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr5:52774400-52779000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr5:52774400-52779000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr5:52774400-52779000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:52774400-52779000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:52774400-52779000	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr5:52774400-52779000	Active TSS	Gastric	stomach
44	chr5:52774400-52779000	Active TSS	Psoas Muscle	Psoas
45	chr5:52774400-52779000	Active TSS	A549	lung
46	chr5:52774400-52779200	Active TSS	H9 Cell Line	embryonic stem cell
47	chr5:52774400-52779200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr5:52774400-52779200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:52774400-52779400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr5:52774600-52776600	Active TSS	Brain Anterior Caudate	brain

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